Mutation Burden file and manual curation
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twtoal ▴ 10
@twtoal-15473
Last seen 4 months ago
United States

Is the mutation burden file produced by Dx.R affected at all by the purity/ploidy selection in the manual curation .csv file?

 

purecn mutation_burden manual_curation • 1.1k views
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@markusriester-9875
Last seen 2.4 years ago
United States

It affects the posterior probabilities of the germline vs somatic classification, but these are fairly robust to errors in purity and ploidy. So if you don't see a difference, that's not unexpected. 

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twtoal ▴ 10
@twtoal-15473
Last seen 4 months ago
United States

Okay, I'm just working on some reorganization to my pipeline.  I've decided to duplicate all the PureCN.R output files, one set prior to manual curation and the second after it.  I think I'll run Dx.R on the manually curated output, no need to run it on the initial output.

 

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